Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 2Z82
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A THR 2.8 9.7 + - - -
175A SER* 3.2 19.7 - - - +
176A LEU 2.8 28.6 + - - +
197A ILE* 3.7 1.0 - - - -
198A ARG* 1.3 83.5 - - + +
200A ILE* 1.3 62.9 + - - +
201A HIS* 3.1 29.7 + - - -
222A SER 4.9 1.7 - - - +
223A SER* 3.8 6.8 - - - +
225A ARG* 2.8 30.0 + - - -
250A PRO* 5.2 0.9 - - - +
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.2 11.4 - - + +
179A LEU* 4.3 21.8 - - + +
194A LEU* 4.9 6.1 - - + +
197A ILE* 3.4 47.3 - - + -
199A ASP* 1.3 71.9 - - - +
201A HIS* 1.3 62.6 + - - +
202A HIS 3.8 24.0 - - - +
203A LEU* 4.0 17.3 - - + -
220A ILE* 5.0 3.1 - - + -
223A SER* 3.1 20.7 + - - +
224A VAL* 3.1 20.5 - - + +
225A ARG* 3.0 23.8 + - - -
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Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 6.1 1.4 - - - -
176A LEU 3.0 14.8 + - - -
177A ASN* 3.1 38.7 + - + +
199A ASP* 3.1 29.3 + - - -
200A ILE* 1.3 71.9 - - - +
202A HIS* 1.3 57.7 + - + +
225A ARG* 3.4 35.8 + - - +
226A TYR* 3.0 28.8 + - - +
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN 3.0 14.3 + - - +
178A GLU* 3.2 23.9 + - + +
179A LEU 3.0 25.6 + - - +
200A ILE* 3.8 2.6 - - - +
201A HIS* 1.3 79.4 - - + +
203A LEU* 1.3 65.9 + - - +
204A THR* 2.9 24.6 + - - -
226A TYR* 3.3 38.3 - + + -
228A GLU* 3.0 25.9 + - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.3 35.2 - - + +
181A ILE* 4.4 3.4 - - + -
194A LEU* 5.3 3.6 - - + -
200A ILE* 4.0 10.0 - - + +
201A HIS 4.3 0.2 - - - -
202A HIS* 1.3 72.5 - - - +
204A THR* 1.3 60.0 + - - +
205A LEU* 3.5 37.7 - - + -
216A ILE* 5.5 0.4 - - + -
220A ILE* 3.8 19.3 - - + -
224A VAL* 3.4 36.1 - - + -
226A TYR 2.8 11.4 + - - +
227A LEU* 3.6 15.2 - - + +
228A GLU 2.8 26.3 + - - +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 4.1 6.8 + - - -
179A LEU 3.1 7.5 + - - -
180A GLU* 3.3 19.0 - - + +
181A ILE 2.9 28.2 + - - +
202A HIS* 2.9 29.8 + - - -
203A LEU* 1.3 72.3 - - - +
205A LEU* 1.3 62.4 + - - +
206A HIS* 3.8 22.9 - - + +
228A GLU* 3.5 13.6 + - - +
230A ARG* 4.0 20.6 - - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.4 32.3 - - + +
194A LEU* 6.0 1.6 - - + -
203A LEU* 3.5 37.4 + - + -
204A THR* 1.3 73.8 - - - +
206A HIS* 1.3 63.7 + - - +
207A LEU* 3.7 12.3 + - + -
213A LEU* 5.3 1.1 - - + -
216A ILE* 3.8 40.2 - - + -
227A LEU* 4.4 9.9 - - + -
228A GLU 2.9 9.1 + - - +
229A LEU* 3.7 23.9 - - + +
230A ARG* 2.9 25.5 + - - +
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.0 35.5 + - + -
181A ILE 3.1 17.6 + - - -
182A LYS* 3.8 39.0 - - + -
183A ALA* 3.0 27.0 + - - +
184A LEU* 3.7 15.9 - - + +
204A THR* 3.8 10.1 - - + +
205A LEU* 1.3 76.1 - - - +
207A LEU* 1.3 61.9 + - - +
230A ARG* 3.5 36.2 - - + +
231A ASP* 4.6 7.1 + - - -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA* 4.0 11.9 - - + +
184A LEU* 3.6 3.4 - - - -
186A LEU* 3.9 29.2 - - + -
205A LEU* 3.7 14.6 + - + -
206A HIS* 1.3 80.4 - - - +
208A SER* 1.3 60.6 + - - +
209A GLU 3.6 18.6 - - - +
212A PHE* 5.4 1.6 - - + +
213A LEU* 4.2 26.9 - - + +
216A ILE* 4.1 24.2 - - + -
229A LEU* 4.3 9.9 - - + -
230A ARG 3.2 4.8 + - - -
231A ASP 3.0 18.7 - - - +
232A THR* 3.0 20.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il